Contacts of the helix formed by residues 15 - 26 (chain D) in PDB entry 1MN8
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 15 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D LEU* 3.0 40.3 + - + +
12D THR 3.4 3.4 - - - -
13D LEU 3.1 0.2 - - - -
14D GLY* 1.3 81.9 + - - +
16D TRP* 1.3 64.2 + - - +
17D LYS 3.3 2.9 - - - -
18D ASP* 3.0 21.1 + - - +
19D VAL* 3.1 10.9 + - - +
96D TRP* 3.3 63.5 + + + +
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Residues in contact with TRP 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 6.3 0.7 - - - -
17C LYS* 5.1 0.9 - - - -
12D THR 3.1 22.6 + - - -
13D LEU* 3.4 20.1 + - + +
14D GLY 3.5 1.0 - - - -
15D HIS* 1.3 78.4 - - - +
17D LYS* 1.3 70.3 + - + +
19D VAL* 3.1 14.9 + - + +
20D GLU* 2.9 52.6 + - + +
30D VAL* 3.6 36.7 + - + -
31D LYS* 3.9 1.1 - - - +
32D LYS* 3.4 55.8 - - + +
35D TRP* 3.6 50.5 - + + -
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Residues in contact with LYS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 5.7 6.7 - - - +
16C TRP* 5.2 1.0 - - - +
17C LYS* 2.9 18.4 - - - +
20C GLU* 2.7 29.9 + - - -
29C ASP* 6.1 0.9 - - - -
15D HIS 3.3 1.0 - - - -
16D TRP* 1.3 84.5 - - + +
18D ASP* 1.3 61.8 + - - +
20D GLU* 2.8 29.8 + - - +
21D ARG* 3.1 29.7 + - + +
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Residues in contact with ASP 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D HIS* 3.0 17.7 + - - +
17D LYS* 1.3 74.7 - - - +
19D VAL* 1.3 66.1 + - - +
21D ARG* 3.2 19.9 + - - +
22D ILE* 2.9 36.5 + - + +
94D PRO* 4.8 3.4 - - + +
95D PRO* 5.6 1.4 - - - +
96D TRP* 2.9 35.3 + - + +
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Residues in contact with VAL 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D THR* 3.7 25.6 - - + +
15D HIS 3.5 11.7 - - - +
16D TRP* 3.1 25.7 + - + +
18D ASP* 1.3 75.0 - - - +
20D GLU* 1.3 58.6 + - - +
22D ILE* 3.2 8.4 + - - +
23D ALA* 2.9 28.1 + - - +
30D VAL* 4.2 5.8 - - + -
35D TRP* 3.8 19.3 - - + -
85D THR* 3.8 17.1 + - - +
89D LEU* 4.6 5.8 - - + -
96D TRP* 3.9 21.3 - - + -
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Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LYS* 2.7 30.4 + - - -
20C GLU* 4.1 3.1 - - - +
24C HIS* 5.3 3.5 + - - +
16D TRP* 2.9 47.2 + - + +
17D LYS* 2.8 40.3 + - - +
18D ASP 3.3 0.2 - - - -
19D VAL* 1.3 76.4 - - - +
21D ARG* 1.3 57.0 + - - +
23D ALA* 3.3 6.2 + - - +
24D HIS* 2.9 51.3 + - + +
29D ASP* 5.4 1.0 - - - +
30D VAL* 4.6 11.6 - - - +
31D LYS* 5.5 1.6 + - - -
32D LYS* 5.4 0.2 + - - -
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Residues in contact with ARG 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C HIS* 3.6 31.3 + - + +
29C ASP* 4.0 31.8 + - - +
17D LYS* 3.1 19.0 + - - +
18D ASP* 3.6 21.0 + - - +
20D GLU* 1.3 78.5 - - - +
22D ILE* 1.3 64.5 + - + +
24D HIS* 3.3 2.1 + - - +
25D ASN* 3.0 23.7 + - - +
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Residues in contact with ILE 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ASP* 2.9 29.4 + - + +
19D VAL* 3.7 4.0 - - - +
21D ARG* 1.3 78.5 - - + +
23D ALA* 1.3 62.9 + - - +
25D ASN* 3.3 8.0 + - - +
26D GLN* 3.3 22.3 + - - +
85D THR* 4.5 7.6 - - - +
88D ALA* 3.8 26.9 - - + -
89D LEU* 3.5 35.0 - - + +
92D ASP 5.5 2.0 - - - +
94D PRO* 4.0 17.9 - - + -
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Residues in contact with ALA 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL 2.9 16.1 + - - +
20D GLU* 3.5 4.7 - - - +
22D ILE* 1.3 76.7 - - - +
24D HIS* 1.3 63.7 + - - +
26D GLN* 2.9 16.0 + - - +
27D SER 3.2 0.2 + - - -
28D VAL* 3.1 29.4 + - + +
29D ASP* 4.5 2.5 - - - -
30D VAL* 4.0 16.2 - - + +
85D THR* 3.3 33.1 + - + +
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Residues in contact with HIS 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LYS 5.3 0.2 + - - -
20C GLU* 5.0 4.2 + - - +
21C ARG* 3.6 30.5 + - + +
24C HIS* 2.7 49.1 + + + -
20D GLU* 2.9 33.6 + - + +
21D ARG 3.3 4.2 + - - +
23D ALA* 1.3 75.3 - - + +
25D ASN* 1.3 57.4 + - - +
27D SER* 2.9 20.7 + - - +
28D VAL 3.3 14.5 + - - +
29D ASP* 2.7 30.9 - - - +
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Residues in contact with ASN 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ARG 3.0 17.4 + - - +
22D ILE* 3.6 7.6 + - - +
23D ALA 3.1 0.2 - - - -
24D HIS* 1.3 78.3 - - - +
26D GLN* 1.3 72.4 + - - +
27D SER* 3.3 3.7 + - - -
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Residues in contact with GLN 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 3.3 12.6 + - - +
23D ALA* 2.9 10.7 + - - +
25D ASN* 1.3 98.6 + - - +
27D SER* 1.3 69.8 + - - +
28D VAL* 3.3 9.1 + - + +
84D VAL* 3.8 25.6 - - + +
85D THR* 5.6 0.4 - - - -
88D ALA* 3.8 28.1 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il